Abstract 3912: cProSite: A web based interactive platform for on-line proteomics and phosphoproteomics data analysis
Authors: Dunrui Wang, Xiaolan Qian, Yi-Chieh Nancy Du, Beatriz Sanchez-Solana, Kailing Chen, Brian Park, Ben Chen, Lisa Jenkins, Jason Luo, Brajendra K. Tripathi, Marian E. Durkin, Douglas R. Lowy
Journal: Cancer Research (2022)

Abstract We have developed a web based interactive platform cProSite (The Cancer Proteogenomic Data Analysis Site). It provides on-line proteomics and phosphoproteomics analysis for the data in The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC), with a focus on tumor and adjacent normal comparisons and correlations between different protein or phosphorylation levels or between protein abundances and mRNA expressions. The web platform is designed for biologists and clinicians wishing to make rapid searches in a user friendly environment. The platform analysis has several advantages compared with standard analytical methods: 1) Faster analysis on-line; 2) More user-friendly; 3) Less need for bioinformatics expertise to perform analyses. Current cProSite includes 11 tumor types*. The web platform includes the following features: 1) Can compare selected protein abundance between tumors and normal adjacent tissues and visualization of fold-changes between paired tumor and control tissue. 2) Can compare selected levels of individual phosphorylation sites or levels of phosphorylation site per protein abundance and visualization of fold-changes between tumors and normal adjacent tissues. 3) Can correlate protein abundance, phosphorylation site levels, or phosphorylation site level per protein abundance between two selected proteins. 4) Can correlate selected protein abundance with its mRNA expression level if the data are available. The cProSite export feature allows users to download the analyzed data. In addition, search outcomes from cProSite can be used for clinical data validation and novel target identification. For example, cProSite can be used to validate findings from other studies; the upregulation of the Hyaluronan Mediated Motility Receptor (Rhamm/HMMR) protein abundance in non-small cell lung adenocarcinoma detected by tissue microarrays was confirmed by cProSite analysis. cProSite can also be used for hypothesis-generation and lead to hypothesis testing. In one example, cProSite identified several upregulated phosphorylation sites in the ECT2 (G2/M phase protein Epithelia Cell Transforming 2) protein in several tumor types. Consistent with that observation, mass spectrometry results showed increased phosphorylation levels from those phosphorylation sites in synchronized lung cancer cell lines in the G2/M phase. * The 11 tumor types in cProSite are: breast cancer, colon cancer, head and neck cancer, liver cancer, kidney cancer, lung adenocarcinoma, lung squamous carcinoma, ovarian cancer, pancreatic ductal adenocarcinoma, stomach cancer, and uterine cancer. Citation Format: Dunrui Wang, Xiaolan Qian, Yi-Chieh Nancy Du, Beatriz Sanchez-Solana, Kailing Chen, Brian Park, Ben Chen, Lisa Jenkins, Jason Luo, Brajendra K. Tripathi, Marian E. Durkin, Douglas R. Lowy. cProSite: A web based interactive platform for on-line proteomics and phosphoproteomics data analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3912.